Starting phenix.real_space_refine on Tue Sep 24 11:36:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xss_22305/09_2024/6xss_22305.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xss_22305/09_2024/6xss_22305.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xss_22305/09_2024/6xss_22305.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xss_22305/09_2024/6xss_22305.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xss_22305/09_2024/6xss_22305.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xss_22305/09_2024/6xss_22305.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 8 5.16 5 C 4956 2.51 5 N 1464 2.21 5 O 1620 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 8048 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2012 Classifications: {'peptide': 260} Link IDs: {'PTRANS': 8, 'TRANS': 251} Restraints were copied for chains: C, B, D Time building chain proxies: 4.05, per 1000 atoms: 0.50 Number of scatterers: 8048 At special positions: 0 Unit cell: (121.119, 121.119, 77.31, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 8 16.00 O 1620 8.00 N 1464 7.00 C 4956 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.29 Conformation dependent library (CDL) restraints added in 1.2 seconds 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2024 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 0 sheets defined 95.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.84 Creating SS restraints... Processing helix chain 'A' and resid 1 through 14 removed outlier: 3.811A pdb=" N VAL A 5 " --> pdb=" O ALA A 1 " (cutoff:3.500A) Processing helix chain 'A' and resid 16 through 31 Processing helix chain 'A' and resid 34 through 49 removed outlier: 3.839A pdb=" N LEU A 47 " --> pdb=" O SER A 43 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU A 48 " --> pdb=" O VAL A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 65 Processing helix chain 'A' and resid 68 through 99 removed outlier: 3.600A pdb=" N ARG A 72 " --> pdb=" O MET A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 124 Processing helix chain 'A' and resid 127 through 155 Processing helix chain 'A' and resid 156 through 180 Processing helix chain 'A' and resid 183 through 211 Processing helix chain 'A' and resid 212 through 236 Processing helix chain 'A' and resid 239 through 260 Processing helix chain 'B' and resid 2 through 14 Processing helix chain 'B' and resid 16 through 31 Processing helix chain 'B' and resid 34 through 49 removed outlier: 3.839A pdb=" N LEU B 47 " --> pdb=" O SER B 43 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU B 48 " --> pdb=" O VAL B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 65 Processing helix chain 'B' and resid 68 through 99 removed outlier: 3.600A pdb=" N ARG B 72 " --> pdb=" O MET B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 124 Processing helix chain 'B' and resid 127 through 155 Processing helix chain 'B' and resid 156 through 180 Processing helix chain 'B' and resid 183 through 211 Processing helix chain 'B' and resid 212 through 236 Processing helix chain 'B' and resid 239 through 260 Processing helix chain 'C' and resid 2 through 14 Processing helix chain 'C' and resid 16 through 31 Processing helix chain 'C' and resid 34 through 49 removed outlier: 3.839A pdb=" N LEU C 47 " --> pdb=" O SER C 43 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU C 48 " --> pdb=" O VAL C 44 " (cutoff:3.500A) Processing helix chain 'C' and resid 50 through 65 Processing helix chain 'C' and resid 68 through 99 removed outlier: 3.600A pdb=" N ARG C 72 " --> pdb=" O MET C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 124 Processing helix chain 'C' and resid 127 through 155 Processing helix chain 'C' and resid 156 through 180 Processing helix chain 'C' and resid 183 through 211 Processing helix chain 'C' and resid 212 through 236 Processing helix chain 'C' and resid 239 through 260 Processing helix chain 'D' and resid 2 through 14 Processing helix chain 'D' and resid 16 through 31 Processing helix chain 'D' and resid 34 through 49 removed outlier: 3.839A pdb=" N LEU D 47 " --> pdb=" O SER D 43 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU D 48 " --> pdb=" O VAL D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 50 through 65 Processing helix chain 'D' and resid 68 through 99 removed outlier: 3.600A pdb=" N ARG D 72 " --> pdb=" O MET D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 124 Processing helix chain 'D' and resid 127 through 155 Processing helix chain 'D' and resid 156 through 180 Processing helix chain 'D' and resid 183 through 211 Processing helix chain 'D' and resid 212 through 236 Processing helix chain 'D' and resid 239 through 260 804 hydrogen bonds defined for protein. 2412 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.40 Time building geometry restraints manager: 2.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2960 1.34 - 1.46: 365 1.46 - 1.57: 4755 1.57 - 1.69: 0 1.69 - 1.80: 16 Bond restraints: 8096 Sorted by residual: bond pdb=" N ASN A 15 " pdb=" CA ASN A 15 " ideal model delta sigma weight residual 1.459 1.472 -0.013 1.32e-02 5.74e+03 9.92e-01 bond pdb=" N ASN B 15 " pdb=" CA ASN B 15 " ideal model delta sigma weight residual 1.459 1.472 -0.013 1.32e-02 5.74e+03 9.81e-01 bond pdb=" N ASN C 15 " pdb=" CA ASN C 15 " ideal model delta sigma weight residual 1.459 1.472 -0.013 1.32e-02 5.74e+03 9.63e-01 bond pdb=" N ASN D 15 " pdb=" CA ASN D 15 " ideal model delta sigma weight residual 1.459 1.471 -0.013 1.32e-02 5.74e+03 9.34e-01 bond pdb=" C GLY D 49 " pdb=" O GLY D 49 " ideal model delta sigma weight residual 1.240 1.229 0.012 1.29e-02 6.01e+03 7.97e-01 ... (remaining 8091 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.72: 10856 2.72 - 5.44: 65 5.44 - 8.16: 7 8.16 - 10.88: 0 10.88 - 13.60: 4 Bond angle restraints: 10932 Sorted by residual: angle pdb=" CA LEU A 222 " pdb=" CB LEU A 222 " pdb=" CG LEU A 222 " ideal model delta sigma weight residual 116.30 129.90 -13.60 3.50e+00 8.16e-02 1.51e+01 angle pdb=" CA LEU D 222 " pdb=" CB LEU D 222 " pdb=" CG LEU D 222 " ideal model delta sigma weight residual 116.30 129.89 -13.59 3.50e+00 8.16e-02 1.51e+01 angle pdb=" CA LEU C 222 " pdb=" CB LEU C 222 " pdb=" CG LEU C 222 " ideal model delta sigma weight residual 116.30 129.89 -13.59 3.50e+00 8.16e-02 1.51e+01 angle pdb=" CA LEU B 222 " pdb=" CB LEU B 222 " pdb=" CG LEU B 222 " ideal model delta sigma weight residual 116.30 129.84 -13.54 3.50e+00 8.16e-02 1.50e+01 angle pdb=" N GLY C 49 " pdb=" CA GLY C 49 " pdb=" C GLY C 49 " ideal model delta sigma weight residual 114.85 110.60 4.25 1.35e+00 5.49e-01 9.90e+00 ... (remaining 10927 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.34: 4804 17.34 - 34.68: 360 34.68 - 52.02: 40 52.02 - 69.37: 4 69.37 - 86.71: 12 Dihedral angle restraints: 5220 sinusoidal: 2156 harmonic: 3064 Sorted by residual: dihedral pdb=" N ASN C 15 " pdb=" C ASN C 15 " pdb=" CA ASN C 15 " pdb=" CB ASN C 15 " ideal model delta harmonic sigma weight residual 122.80 132.00 -9.20 0 2.50e+00 1.60e-01 1.35e+01 dihedral pdb=" N ASN A 15 " pdb=" C ASN A 15 " pdb=" CA ASN A 15 " pdb=" CB ASN A 15 " ideal model delta harmonic sigma weight residual 122.80 131.99 -9.19 0 2.50e+00 1.60e-01 1.35e+01 dihedral pdb=" N ASN B 15 " pdb=" C ASN B 15 " pdb=" CA ASN B 15 " pdb=" CB ASN B 15 " ideal model delta harmonic sigma weight residual 122.80 131.96 -9.16 0 2.50e+00 1.60e-01 1.34e+01 ... (remaining 5217 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 1198 0.066 - 0.131: 94 0.131 - 0.197: 4 0.197 - 0.263: 0 0.263 - 0.328: 4 Chirality restraints: 1300 Sorted by residual: chirality pdb=" CA ASN C 15 " pdb=" N ASN C 15 " pdb=" C ASN C 15 " pdb=" CB ASN C 15 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.69e+00 chirality pdb=" CA ASN A 15 " pdb=" N ASN A 15 " pdb=" C ASN A 15 " pdb=" CB ASN A 15 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.68e+00 chirality pdb=" CA ASN B 15 " pdb=" N ASN B 15 " pdb=" C ASN B 15 " pdb=" CB ASN B 15 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.63e+00 ... (remaining 1297 not shown) Planarity restraints: 1468 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU D 14 " 0.006 2.00e-02 2.50e+03 1.31e-02 1.72e+00 pdb=" C LEU D 14 " -0.023 2.00e-02 2.50e+03 pdb=" O LEU D 14 " 0.009 2.00e-02 2.50e+03 pdb=" N ASN D 15 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU C 14 " 0.006 2.00e-02 2.50e+03 1.30e-02 1.70e+00 pdb=" C LEU C 14 " -0.023 2.00e-02 2.50e+03 pdb=" O LEU C 14 " 0.009 2.00e-02 2.50e+03 pdb=" N ASN C 15 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 14 " 0.006 2.00e-02 2.50e+03 1.29e-02 1.66e+00 pdb=" C LEU A 14 " -0.022 2.00e-02 2.50e+03 pdb=" O LEU A 14 " 0.009 2.00e-02 2.50e+03 pdb=" N ASN A 15 " 0.008 2.00e-02 2.50e+03 ... (remaining 1465 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.45: 49 2.45 - 3.07: 5477 3.07 - 3.68: 12994 3.68 - 4.29: 17762 4.29 - 4.90: 28573 Nonbonded interactions: 64855 Sorted by model distance: nonbonded pdb=" CB ALA D 94 " pdb=" CD2 LEU D 148 " model vdw 1.843 3.880 nonbonded pdb=" CB ALA A 94 " pdb=" CD2 LEU A 148 " model vdw 1.843 3.880 nonbonded pdb=" CB ALA C 94 " pdb=" CD2 LEU C 148 " model vdw 1.843 3.880 nonbonded pdb=" CB ALA B 94 " pdb=" CD2 LEU B 148 " model vdw 1.844 3.880 nonbonded pdb=" NH2 ARG A 83 " pdb=" OE1 GLU A 142 " model vdw 1.982 3.120 ... (remaining 64850 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 21.350 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 8096 Z= 0.176 Angle : 0.628 13.605 10932 Z= 0.356 Chirality : 0.038 0.328 1300 Planarity : 0.003 0.024 1468 Dihedral : 12.310 86.708 3196 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 28.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.23), residues: 1032 helix: 0.08 (0.14), residues: 976 sheet: None (None), residues: 0 loop : -3.14 (1.01), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 4 TYR 0.002 0.001 TYR D 24 ARG 0.006 0.000 ARG B 123 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 307 time to evaluate : 0.979 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 ASN cc_start: 0.8100 (m-40) cc_final: 0.7624 (t0) REVERT: A 60 LYS cc_start: 0.8486 (mmtt) cc_final: 0.8225 (mmtm) REVERT: A 119 GLU cc_start: 0.7987 (tm-30) cc_final: 0.7609 (tm-30) REVERT: A 168 ARG cc_start: 0.7831 (mtt180) cc_final: 0.7436 (ttp-110) REVERT: A 180 ASN cc_start: 0.7917 (m-40) cc_final: 0.7545 (p0) REVERT: A 191 LYS cc_start: 0.9054 (mttt) cc_final: 0.8101 (mmmt) REVERT: A 195 GLU cc_start: 0.8468 (mm-30) cc_final: 0.8076 (mm-30) REVERT: A 209 LYS cc_start: 0.8246 (mttt) cc_final: 0.7892 (tmmt) REVERT: A 210 THR cc_start: 0.6614 (m) cc_final: 0.6301 (p) REVERT: B 31 ASP cc_start: 0.8454 (t0) cc_final: 0.8217 (t0) REVERT: B 60 LYS cc_start: 0.8389 (mmtt) cc_final: 0.8171 (mmtm) REVERT: B 154 THR cc_start: 0.6910 (p) cc_final: 0.6669 (t) REVERT: B 168 ARG cc_start: 0.7799 (mtt180) cc_final: 0.7465 (ttp-110) REVERT: B 180 ASN cc_start: 0.7867 (m-40) cc_final: 0.7468 (p0) REVERT: B 191 LYS cc_start: 0.9054 (mttt) cc_final: 0.8037 (mmmt) REVERT: B 195 GLU cc_start: 0.8463 (mm-30) cc_final: 0.8049 (mm-30) REVERT: B 210 THR cc_start: 0.6841 (m) cc_final: 0.6595 (p) REVERT: B 224 ARG cc_start: 0.8521 (mtt90) cc_final: 0.7813 (mtp-110) REVERT: C 60 LYS cc_start: 0.8401 (mmtt) cc_final: 0.8135 (mmmt) REVERT: C 168 ARG cc_start: 0.8035 (mtt180) cc_final: 0.7152 (ttp-110) REVERT: C 180 ASN cc_start: 0.7347 (m-40) cc_final: 0.7145 (p0) REVERT: C 195 GLU cc_start: 0.8563 (mm-30) cc_final: 0.8081 (mm-30) REVERT: C 224 ARG cc_start: 0.8344 (mtt90) cc_final: 0.7877 (tmt-80) REVERT: C 254 GLN cc_start: 0.8336 (mt0) cc_final: 0.7708 (tm-30) REVERT: D 15 ASN cc_start: 0.8079 (m-40) cc_final: 0.7650 (t0) REVERT: D 119 GLU cc_start: 0.8035 (tm-30) cc_final: 0.7599 (tm-30) REVERT: D 168 ARG cc_start: 0.7835 (mtt180) cc_final: 0.7321 (ttp-110) REVERT: D 180 ASN cc_start: 0.7872 (m-40) cc_final: 0.7525 (p0) REVERT: D 191 LYS cc_start: 0.9031 (mttt) cc_final: 0.8042 (mmmt) REVERT: D 195 GLU cc_start: 0.8498 (mm-30) cc_final: 0.8098 (mm-30) REVERT: D 201 VAL cc_start: 0.9307 (m) cc_final: 0.9104 (m) REVERT: D 224 ARG cc_start: 0.8439 (mtt90) cc_final: 0.7784 (mtp-110) outliers start: 0 outliers final: 0 residues processed: 307 average time/residue: 0.3136 time to fit residues: 116.1821 Evaluate side-chains 159 residues out of total 824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 159 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 87 optimal weight: 5.9990 chunk 78 optimal weight: 0.6980 chunk 43 optimal weight: 6.9990 chunk 26 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 42 optimal weight: 6.9990 chunk 81 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 94 optimal weight: 5.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 ASN C 131 ASN C 234 GLN D 131 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.2910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8096 Z= 0.247 Angle : 0.695 10.934 10932 Z= 0.334 Chirality : 0.038 0.146 1300 Planarity : 0.004 0.042 1468 Dihedral : 3.438 11.893 1148 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 15.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.46 % Allowed : 13.71 % Favored : 84.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.25), residues: 1032 helix: 1.16 (0.15), residues: 988 sheet: None (None), residues: 0 loop : -4.17 (1.03), residues: 44 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 4 TYR 0.011 0.003 TYR A 24 ARG 0.007 0.001 ARG B 179 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 179 time to evaluate : 0.974 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 ASN cc_start: 0.8365 (m-40) cc_final: 0.7794 (t0) REVERT: A 131 ASN cc_start: 0.8329 (OUTLIER) cc_final: 0.8064 (t0) REVERT: A 168 ARG cc_start: 0.7827 (mtt180) cc_final: 0.7155 (ttp-110) REVERT: A 180 ASN cc_start: 0.7910 (m-40) cc_final: 0.7677 (p0) REVERT: A 195 GLU cc_start: 0.8469 (mm-30) cc_final: 0.8074 (mm-30) REVERT: A 224 ARG cc_start: 0.8563 (mtt90) cc_final: 0.7846 (mtp-110) REVERT: B 154 THR cc_start: 0.6845 (p) cc_final: 0.6623 (t) REVERT: B 168 ARG cc_start: 0.7766 (mtt180) cc_final: 0.7248 (ttp-110) REVERT: B 180 ASN cc_start: 0.7838 (m-40) cc_final: 0.7448 (p0) REVERT: B 195 GLU cc_start: 0.8460 (mm-30) cc_final: 0.8072 (mm-30) REVERT: B 210 THR cc_start: 0.6770 (m) cc_final: 0.6555 (p) REVERT: B 224 ARG cc_start: 0.8522 (mtt90) cc_final: 0.7831 (mtp-110) REVERT: C 69 ASP cc_start: 0.8413 (p0) cc_final: 0.8133 (p0) REVERT: C 168 ARG cc_start: 0.8074 (mtt180) cc_final: 0.7082 (ttp-110) REVERT: C 195 GLU cc_start: 0.8548 (mm-30) cc_final: 0.8097 (mm-30) REVERT: C 224 ARG cc_start: 0.8345 (mtt90) cc_final: 0.7884 (tmt-80) REVERT: D 15 ASN cc_start: 0.8401 (m-40) cc_final: 0.7797 (t0) REVERT: D 168 ARG cc_start: 0.7691 (mtt180) cc_final: 0.7185 (ttp-110) REVERT: D 180 ASN cc_start: 0.7848 (m-40) cc_final: 0.7505 (p0) REVERT: D 195 GLU cc_start: 0.8506 (mm-30) cc_final: 0.8137 (mm-30) REVERT: D 224 ARG cc_start: 0.8451 (mtt90) cc_final: 0.7845 (mtp-110) outliers start: 12 outliers final: 6 residues processed: 181 average time/residue: 0.2522 time to fit residues: 58.4208 Evaluate side-chains 142 residues out of total 824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 135 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 131 ASN Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain D residue 113 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 52 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 chunk 78 optimal weight: 0.7980 chunk 64 optimal weight: 8.9990 chunk 26 optimal weight: 0.8980 chunk 94 optimal weight: 9.9990 chunk 102 optimal weight: 4.9990 chunk 84 optimal weight: 5.9990 chunk 93 optimal weight: 6.9990 chunk 32 optimal weight: 8.9990 chunk 75 optimal weight: 4.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 187 ASN D 131 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.3501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8096 Z= 0.231 Angle : 0.663 11.051 10932 Z= 0.316 Chirality : 0.035 0.142 1300 Planarity : 0.004 0.043 1468 Dihedral : 3.402 12.207 1148 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 15.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 3.40 % Allowed : 14.56 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.17 (0.25), residues: 1032 helix: 1.70 (0.15), residues: 976 sheet: None (None), residues: 0 loop : -3.04 (0.95), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 4 TYR 0.008 0.002 TYR D 24 ARG 0.007 0.000 ARG B 102 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 156 time to evaluate : 0.954 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 15 ASN cc_start: 0.8463 (m-40) cc_final: 0.7881 (t0) REVERT: A 168 ARG cc_start: 0.7707 (mtt180) cc_final: 0.7223 (ttp-110) REVERT: A 195 GLU cc_start: 0.8405 (mm-30) cc_final: 0.8046 (mm-30) REVERT: A 224 ARG cc_start: 0.8560 (mtt90) cc_final: 0.7829 (mtp-110) REVERT: B 123 ARG cc_start: 0.8147 (tpm170) cc_final: 0.7721 (mmm-85) REVERT: B 154 THR cc_start: 0.6833 (p) cc_final: 0.6615 (t) REVERT: B 168 ARG cc_start: 0.7672 (mtt180) cc_final: 0.7213 (ttp-110) REVERT: B 180 ASN cc_start: 0.7884 (m-40) cc_final: 0.7420 (p0) REVERT: B 195 GLU cc_start: 0.8452 (mm-30) cc_final: 0.8081 (mm-30) REVERT: B 210 THR cc_start: 0.6817 (m) cc_final: 0.6605 (p) REVERT: B 224 ARG cc_start: 0.8550 (mtt90) cc_final: 0.7868 (mtp-110) REVERT: C 69 ASP cc_start: 0.8484 (p0) cc_final: 0.8221 (p0) REVERT: C 149 GLU cc_start: 0.8229 (pt0) cc_final: 0.7774 (tm-30) REVERT: C 168 ARG cc_start: 0.7972 (mtt180) cc_final: 0.6970 (ttp-110) REVERT: C 195 GLU cc_start: 0.8593 (mm-30) cc_final: 0.8146 (mm-30) REVERT: C 224 ARG cc_start: 0.8351 (mtt90) cc_final: 0.7877 (tmt-80) REVERT: C 254 GLN cc_start: 0.8277 (mt0) cc_final: 0.7671 (tm-30) REVERT: D 15 ASN cc_start: 0.8486 (m-40) cc_final: 0.7882 (t0) REVERT: D 168 ARG cc_start: 0.7668 (mtt180) cc_final: 0.7143 (ttp-110) REVERT: D 180 ASN cc_start: 0.7833 (m-40) cc_final: 0.7486 (p0) REVERT: D 195 GLU cc_start: 0.8511 (mm-30) cc_final: 0.8109 (mm-30) REVERT: D 224 ARG cc_start: 0.8460 (mtt90) cc_final: 0.7814 (mtp-110) outliers start: 28 outliers final: 19 residues processed: 166 average time/residue: 0.2353 time to fit residues: 50.6547 Evaluate side-chains 149 residues out of total 824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 130 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 228 GLU Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 228 GLU Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 238 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 93 optimal weight: 0.8980 chunk 71 optimal weight: 7.9990 chunk 49 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 45 optimal weight: 6.9990 chunk 63 optimal weight: 5.9990 chunk 94 optimal weight: 5.9990 chunk 100 optimal weight: 7.9990 chunk 89 optimal weight: 0.9980 chunk 27 optimal weight: 0.7980 chunk 83 optimal weight: 5.9990 overall best weight: 2.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 187 ASN ** B 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.3918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 8096 Z= 0.299 Angle : 0.695 10.716 10932 Z= 0.340 Chirality : 0.036 0.145 1300 Planarity : 0.005 0.047 1468 Dihedral : 3.445 12.441 1148 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 17.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 4.61 % Allowed : 17.72 % Favored : 77.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.17 (0.25), residues: 1032 helix: 1.75 (0.15), residues: 984 sheet: None (None), residues: 0 loop : -4.92 (0.66), residues: 48 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 4 TYR 0.008 0.002 TYR D 24 ARG 0.007 0.001 ARG B 102 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 143 time to evaluate : 0.995 Fit side-chains revert: symmetry clash REVERT: A 15 ASN cc_start: 0.8635 (m-40) cc_final: 0.8031 (t0) REVERT: A 168 ARG cc_start: 0.7748 (mtt180) cc_final: 0.7191 (ttp-110) REVERT: A 195 GLU cc_start: 0.8517 (mm-30) cc_final: 0.8165 (mm-30) REVERT: A 224 ARG cc_start: 0.8597 (mtt90) cc_final: 0.7783 (mtp-110) REVERT: B 154 THR cc_start: 0.6853 (p) cc_final: 0.6628 (t) REVERT: B 168 ARG cc_start: 0.7706 (mtt180) cc_final: 0.7181 (ttp-110) REVERT: B 180 ASN cc_start: 0.7962 (m-40) cc_final: 0.7467 (p0) REVERT: B 195 GLU cc_start: 0.8501 (mm-30) cc_final: 0.8136 (mm-30) REVERT: B 224 ARG cc_start: 0.8585 (mtt90) cc_final: 0.7839 (mtp-110) REVERT: C 149 GLU cc_start: 0.8262 (pt0) cc_final: 0.7722 (tm-30) REVERT: C 165 GLU cc_start: 0.8881 (mt-10) cc_final: 0.8578 (pt0) REVERT: C 168 ARG cc_start: 0.7895 (mtt180) cc_final: 0.6831 (ttp-110) REVERT: C 195 GLU cc_start: 0.8600 (mm-30) cc_final: 0.8187 (mm-30) REVERT: C 224 ARG cc_start: 0.8417 (mtt90) cc_final: 0.7743 (mtp-110) REVERT: D 15 ASN cc_start: 0.8628 (m-40) cc_final: 0.8069 (t0) REVERT: D 168 ARG cc_start: 0.7733 (mtt180) cc_final: 0.7101 (ttp-110) REVERT: D 180 ASN cc_start: 0.7979 (m-40) cc_final: 0.7538 (p0) REVERT: D 195 GLU cc_start: 0.8542 (mm-30) cc_final: 0.8158 (mm-30) REVERT: D 224 ARG cc_start: 0.8492 (mtt90) cc_final: 0.7808 (mtp-110) outliers start: 38 outliers final: 24 residues processed: 158 average time/residue: 0.2296 time to fit residues: 47.3532 Evaluate side-chains 147 residues out of total 824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 123 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 228 GLU Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 249 ILE Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 238 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 57 optimal weight: 5.9990 chunk 1 optimal weight: 0.6980 chunk 74 optimal weight: 3.9990 chunk 41 optimal weight: 7.9990 chunk 85 optimal weight: 4.9990 chunk 69 optimal weight: 3.9990 chunk 0 optimal weight: 1.9990 chunk 51 optimal weight: 6.9990 chunk 90 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 chunk 33 optimal weight: 0.9980 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 92 GLN B 187 ASN D 92 GLN D 187 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.4125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8096 Z= 0.259 Angle : 0.673 11.213 10932 Z= 0.324 Chirality : 0.035 0.148 1300 Planarity : 0.005 0.046 1468 Dihedral : 3.439 12.173 1148 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 16.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 4.25 % Allowed : 18.57 % Favored : 77.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.38 (0.25), residues: 1032 helix: 1.88 (0.15), residues: 988 sheet: None (None), residues: 0 loop : -5.41 (0.66), residues: 44 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 4 TYR 0.008 0.002 TYR D 24 ARG 0.009 0.000 ARG D 179 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 140 time to evaluate : 1.007 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 15 ASN cc_start: 0.8681 (m-40) cc_final: 0.8245 (t0) REVERT: A 168 ARG cc_start: 0.7677 (mtt180) cc_final: 0.7096 (ttp-110) REVERT: A 195 GLU cc_start: 0.8490 (mm-30) cc_final: 0.8131 (mm-30) REVERT: A 224 ARG cc_start: 0.8632 (mtt90) cc_final: 0.7818 (mtp-110) REVERT: B 154 THR cc_start: 0.6896 (p) cc_final: 0.6665 (t) REVERT: B 168 ARG cc_start: 0.7688 (mtt180) cc_final: 0.7156 (ttp-110) REVERT: B 180 ASN cc_start: 0.7930 (m-40) cc_final: 0.7381 (p0) REVERT: B 195 GLU cc_start: 0.8513 (mm-30) cc_final: 0.8126 (mm-30) REVERT: B 224 ARG cc_start: 0.8601 (mtt90) cc_final: 0.7617 (mtp-110) REVERT: C 131 ASN cc_start: 0.8033 (m-40) cc_final: 0.7587 (m-40) REVERT: C 154 THR cc_start: 0.6336 (p) cc_final: 0.6090 (t) REVERT: C 165 GLU cc_start: 0.8827 (mt-10) cc_final: 0.8472 (pt0) REVERT: C 168 ARG cc_start: 0.7769 (mtt180) cc_final: 0.6726 (ttp-110) REVERT: C 195 GLU cc_start: 0.8604 (mm-30) cc_final: 0.8173 (mm-30) REVERT: C 224 ARG cc_start: 0.8425 (mtt90) cc_final: 0.7754 (mtp-110) REVERT: D 15 ASN cc_start: 0.8675 (m-40) cc_final: 0.8274 (t0) REVERT: D 168 ARG cc_start: 0.7664 (mtt180) cc_final: 0.6978 (ttp-110) REVERT: D 180 ASN cc_start: 0.8044 (m-40) cc_final: 0.7533 (p0) REVERT: D 195 GLU cc_start: 0.8530 (mm-30) cc_final: 0.8142 (mm-30) REVERT: D 224 ARG cc_start: 0.8553 (mtt90) cc_final: 0.7933 (mtp-110) outliers start: 35 outliers final: 22 residues processed: 155 average time/residue: 0.2327 time to fit residues: 47.3169 Evaluate side-chains 144 residues out of total 824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 122 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 183 SER Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 186 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 90 optimal weight: 4.9990 chunk 19 optimal weight: 0.8980 chunk 59 optimal weight: 7.9990 chunk 24 optimal weight: 5.9990 chunk 100 optimal weight: 0.8980 chunk 83 optimal weight: 6.9990 chunk 46 optimal weight: 8.9990 chunk 8 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 52 optimal weight: 0.9980 chunk 97 optimal weight: 5.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 GLN C 15 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.4217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8096 Z= 0.203 Angle : 0.674 11.883 10932 Z= 0.318 Chirality : 0.034 0.128 1300 Planarity : 0.004 0.045 1468 Dihedral : 3.441 12.279 1148 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 14.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Rotamer: Outliers : 2.91 % Allowed : 20.51 % Favored : 76.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.69 (0.25), residues: 1032 helix: 2.07 (0.15), residues: 988 sheet: None (None), residues: 0 loop : -5.31 (0.68), residues: 44 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 4 TYR 0.007 0.002 TYR D 24 ARG 0.007 0.000 ARG D 179 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 146 time to evaluate : 1.058 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 15 ASN cc_start: 0.8656 (m-40) cc_final: 0.8210 (t0) REVERT: A 168 ARG cc_start: 0.7604 (mtt180) cc_final: 0.7016 (ttp-110) REVERT: A 195 GLU cc_start: 0.8474 (mm-30) cc_final: 0.8085 (mm-30) REVERT: A 224 ARG cc_start: 0.8550 (mtt90) cc_final: 0.7472 (mtp-110) REVERT: B 154 THR cc_start: 0.6941 (p) cc_final: 0.6723 (t) REVERT: B 168 ARG cc_start: 0.7622 (mtt180) cc_final: 0.7034 (ttp-110) REVERT: B 180 ASN cc_start: 0.7953 (m-40) cc_final: 0.7442 (p0) REVERT: B 195 GLU cc_start: 0.8484 (mm-30) cc_final: 0.8097 (mm-30) REVERT: B 224 ARG cc_start: 0.8560 (mtt90) cc_final: 0.7818 (mtp-110) REVERT: C 131 ASN cc_start: 0.7976 (m-40) cc_final: 0.7528 (m-40) REVERT: C 154 THR cc_start: 0.6370 (p) cc_final: 0.6134 (t) REVERT: C 165 GLU cc_start: 0.8811 (mt-10) cc_final: 0.8413 (pt0) REVERT: C 168 ARG cc_start: 0.7758 (mtt180) cc_final: 0.6891 (ttp-110) REVERT: C 180 ASN cc_start: 0.8024 (m110) cc_final: 0.7469 (p0) REVERT: C 195 GLU cc_start: 0.8618 (mm-30) cc_final: 0.8166 (mm-30) REVERT: C 224 ARG cc_start: 0.8377 (mtt90) cc_final: 0.7716 (mtp-110) REVERT: D 15 ASN cc_start: 0.8623 (m-40) cc_final: 0.8292 (t0) REVERT: D 168 ARG cc_start: 0.7554 (mtt180) cc_final: 0.6865 (ttp-110) REVERT: D 180 ASN cc_start: 0.7909 (m-40) cc_final: 0.7500 (p0) REVERT: D 195 GLU cc_start: 0.8513 (mm-30) cc_final: 0.8140 (mm-30) REVERT: D 224 ARG cc_start: 0.8531 (mtt90) cc_final: 0.7921 (mtp-110) outliers start: 24 outliers final: 14 residues processed: 156 average time/residue: 0.2310 time to fit residues: 47.0863 Evaluate side-chains 140 residues out of total 824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 126 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 183 SER Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 186 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 11 optimal weight: 10.0000 chunk 57 optimal weight: 4.9990 chunk 73 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 84 optimal weight: 4.9990 chunk 100 optimal weight: 5.9990 chunk 62 optimal weight: 3.9990 chunk 61 optimal weight: 0.5980 chunk 46 optimal weight: 6.9990 chunk 40 optimal weight: 6.9990 chunk 59 optimal weight: 0.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.4412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8096 Z= 0.260 Angle : 0.697 12.268 10932 Z= 0.333 Chirality : 0.036 0.154 1300 Planarity : 0.005 0.044 1468 Dihedral : 3.436 11.941 1148 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 16.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 3.40 % Allowed : 21.60 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.63 (0.25), residues: 1032 helix: 2.05 (0.15), residues: 988 sheet: None (None), residues: 0 loop : -5.60 (0.63), residues: 44 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 4 TYR 0.007 0.002 TYR A 24 ARG 0.012 0.000 ARG A 179 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 132 time to evaluate : 1.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 ASN cc_start: 0.8654 (m-40) cc_final: 0.8269 (t0) REVERT: A 168 ARG cc_start: 0.7623 (mtt180) cc_final: 0.6972 (ttp-110) REVERT: A 195 GLU cc_start: 0.8488 (mm-30) cc_final: 0.8119 (mm-30) REVERT: A 224 ARG cc_start: 0.8562 (mtt90) cc_final: 0.7774 (mtp-110) REVERT: B 154 THR cc_start: 0.6930 (p) cc_final: 0.6715 (t) REVERT: B 168 ARG cc_start: 0.7648 (mtt180) cc_final: 0.7051 (ttp-110) REVERT: B 180 ASN cc_start: 0.8013 (m-40) cc_final: 0.7451 (p0) REVERT: B 195 GLU cc_start: 0.8491 (mm-30) cc_final: 0.8108 (mm-30) REVERT: B 224 ARG cc_start: 0.8558 (mtt90) cc_final: 0.7956 (mtp-110) REVERT: C 131 ASN cc_start: 0.8032 (m-40) cc_final: 0.7557 (m-40) REVERT: C 154 THR cc_start: 0.6461 (p) cc_final: 0.6254 (t) REVERT: C 168 ARG cc_start: 0.7736 (mtt180) cc_final: 0.6851 (ttp-110) REVERT: C 195 GLU cc_start: 0.8684 (mm-30) cc_final: 0.8211 (mm-30) REVERT: C 224 ARG cc_start: 0.8404 (mtt90) cc_final: 0.7763 (mtp-110) REVERT: D 15 ASN cc_start: 0.8665 (m-40) cc_final: 0.8371 (t0) REVERT: D 168 ARG cc_start: 0.7614 (mtt180) cc_final: 0.6925 (ttp-110) REVERT: D 180 ASN cc_start: 0.8049 (m-40) cc_final: 0.7548 (p0) REVERT: D 195 GLU cc_start: 0.8537 (mm-30) cc_final: 0.8194 (mm-30) REVERT: D 224 ARG cc_start: 0.8552 (mtt90) cc_final: 0.7939 (mtp-110) outliers start: 28 outliers final: 19 residues processed: 143 average time/residue: 0.2211 time to fit residues: 41.8860 Evaluate side-chains 139 residues out of total 824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 120 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 183 SER Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 238 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 30 optimal weight: 4.9990 chunk 19 optimal weight: 6.9990 chunk 63 optimal weight: 6.9990 chunk 68 optimal weight: 6.9990 chunk 49 optimal weight: 5.9990 chunk 9 optimal weight: 6.9990 chunk 78 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 chunk 96 optimal weight: 5.9990 chunk 87 optimal weight: 3.9990 chunk 93 optimal weight: 4.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.4624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 8096 Z= 0.325 Angle : 0.735 12.492 10932 Z= 0.360 Chirality : 0.038 0.170 1300 Planarity : 0.005 0.045 1468 Dihedral : 3.499 12.819 1148 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 19.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 4.13 % Allowed : 22.21 % Favored : 73.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.35 (0.24), residues: 1032 helix: 1.89 (0.15), residues: 984 sheet: None (None), residues: 0 loop : -5.64 (0.57), residues: 48 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 4 TYR 0.007 0.003 TYR D 24 ARG 0.012 0.001 ARG A 179 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 129 time to evaluate : 0.977 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 15 ASN cc_start: 0.8686 (m-40) cc_final: 0.8264 (t0) REVERT: A 168 ARG cc_start: 0.7689 (mtt180) cc_final: 0.7041 (ttp-110) REVERT: A 195 GLU cc_start: 0.8515 (mm-30) cc_final: 0.8172 (mm-30) REVERT: A 224 ARG cc_start: 0.8559 (mtt90) cc_final: 0.7764 (mtp-110) REVERT: A 249 ILE cc_start: 0.8387 (mp) cc_final: 0.8070 (mt) REVERT: B 154 THR cc_start: 0.6940 (p) cc_final: 0.6722 (t) REVERT: B 168 ARG cc_start: 0.7675 (mtt180) cc_final: 0.7176 (ttp-110) REVERT: B 180 ASN cc_start: 0.8020 (m-40) cc_final: 0.7437 (p0) REVERT: B 195 GLU cc_start: 0.8550 (mm-30) cc_final: 0.8228 (mm-30) REVERT: B 224 ARG cc_start: 0.8642 (mtt90) cc_final: 0.7962 (mtp-110) REVERT: C 168 ARG cc_start: 0.7740 (mtt180) cc_final: 0.6969 (ttp-110) REVERT: C 195 GLU cc_start: 0.8729 (mm-30) cc_final: 0.8265 (mm-30) REVERT: C 224 ARG cc_start: 0.8418 (mtt90) cc_final: 0.7774 (mtp-110) REVERT: D 15 ASN cc_start: 0.8679 (m-40) cc_final: 0.8368 (t0) REVERT: D 168 ARG cc_start: 0.7644 (mtt180) cc_final: 0.7005 (ttp-110) REVERT: D 180 ASN cc_start: 0.8050 (m-40) cc_final: 0.7459 (p0) REVERT: D 195 GLU cc_start: 0.8562 (mm-30) cc_final: 0.8206 (mm-30) REVERT: D 224 ARG cc_start: 0.8597 (mtt90) cc_final: 0.7885 (mtp-110) outliers start: 34 outliers final: 23 residues processed: 142 average time/residue: 0.2238 time to fit residues: 42.0098 Evaluate side-chains 142 residues out of total 824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 119 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 249 ILE Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 228 GLU Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 238 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 96 optimal weight: 4.9990 chunk 56 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 73 optimal weight: 8.9990 chunk 28 optimal weight: 0.9980 chunk 84 optimal weight: 0.8980 chunk 88 optimal weight: 0.9990 chunk 93 optimal weight: 6.9990 chunk 61 optimal weight: 4.9990 chunk 98 optimal weight: 5.9990 chunk 60 optimal weight: 0.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.4573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8096 Z= 0.207 Angle : 0.722 13.529 10932 Z= 0.339 Chirality : 0.035 0.153 1300 Planarity : 0.004 0.044 1468 Dihedral : 3.496 11.540 1148 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 15.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Rotamer: Outliers : 2.06 % Allowed : 23.67 % Favored : 74.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.63 (0.25), residues: 1032 helix: 2.04 (0.15), residues: 988 sheet: None (None), residues: 0 loop : -5.48 (0.70), residues: 44 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 4 TYR 0.008 0.002 TYR D 24 ARG 0.010 0.000 ARG A 179 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 147 time to evaluate : 1.019 Fit side-chains revert: symmetry clash REVERT: A 15 ASN cc_start: 0.8676 (m-40) cc_final: 0.8368 (t0) REVERT: A 168 ARG cc_start: 0.7586 (mtt180) cc_final: 0.6944 (ttp-110) REVERT: A 224 ARG cc_start: 0.8504 (mtt90) cc_final: 0.7714 (mtp-110) REVERT: B 154 THR cc_start: 0.6918 (p) cc_final: 0.6700 (t) REVERT: B 168 ARG cc_start: 0.7661 (mtt180) cc_final: 0.6996 (ttp-110) REVERT: B 180 ASN cc_start: 0.8004 (m-40) cc_final: 0.7408 (p0) REVERT: B 195 GLU cc_start: 0.8539 (mm-30) cc_final: 0.8176 (mm-30) REVERT: B 224 ARG cc_start: 0.8657 (mtt90) cc_final: 0.7996 (mtp-110) REVERT: C 15 ASN cc_start: 0.8143 (t0) cc_final: 0.7830 (t0) REVERT: C 154 THR cc_start: 0.6507 (p) cc_final: 0.6290 (t) REVERT: C 168 ARG cc_start: 0.7697 (mtt180) cc_final: 0.6831 (ttp-110) REVERT: C 195 GLU cc_start: 0.8677 (mm-30) cc_final: 0.8224 (mm-30) REVERT: C 224 ARG cc_start: 0.8396 (mtt90) cc_final: 0.7723 (mtp-110) REVERT: D 15 ASN cc_start: 0.8628 (m-40) cc_final: 0.8416 (t0) REVERT: D 168 ARG cc_start: 0.7538 (mtt180) cc_final: 0.6876 (ttp-110) REVERT: D 180 ASN cc_start: 0.8007 (m-40) cc_final: 0.7413 (p0) REVERT: D 195 GLU cc_start: 0.8536 (mm-30) cc_final: 0.8190 (mm-30) REVERT: D 224 ARG cc_start: 0.8560 (mtt90) cc_final: 0.7938 (mtp-110) outliers start: 17 outliers final: 12 residues processed: 154 average time/residue: 0.2190 time to fit residues: 44.8604 Evaluate side-chains 141 residues out of total 824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 129 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 183 SER Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 148 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 46 optimal weight: 9.9990 chunk 68 optimal weight: 10.0000 chunk 103 optimal weight: 5.9990 chunk 95 optimal weight: 4.9990 chunk 82 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 63 optimal weight: 0.9990 chunk 50 optimal weight: 5.9990 chunk 65 optimal weight: 7.9990 chunk 87 optimal weight: 6.9990 chunk 25 optimal weight: 8.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.4796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 8096 Z= 0.349 Angle : 0.791 13.076 10932 Z= 0.390 Chirality : 0.040 0.168 1300 Planarity : 0.005 0.053 1468 Dihedral : 3.517 13.963 1148 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 20.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.06 % Allowed : 25.24 % Favored : 72.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.19 (0.24), residues: 1032 helix: 1.77 (0.15), residues: 988 sheet: None (None), residues: 0 loop : -5.81 (0.66), residues: 44 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 4 TYR 0.006 0.002 TYR A 24 ARG 0.014 0.001 ARG D 202 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 125 time to evaluate : 0.943 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 15 ASN cc_start: 0.8704 (m-40) cc_final: 0.8300 (t0) REVERT: A 168 ARG cc_start: 0.7643 (mtt180) cc_final: 0.7016 (ttp-110) REVERT: A 195 GLU cc_start: 0.8337 (mp0) cc_final: 0.7969 (mp0) REVERT: A 224 ARG cc_start: 0.8569 (mtt90) cc_final: 0.7776 (mtp-110) REVERT: B 168 ARG cc_start: 0.7770 (mtt180) cc_final: 0.7165 (ttp-110) REVERT: B 180 ASN cc_start: 0.8032 (m-40) cc_final: 0.7415 (p0) REVERT: B 195 GLU cc_start: 0.8566 (mm-30) cc_final: 0.8211 (mm-30) REVERT: B 224 ARG cc_start: 0.8658 (mtt90) cc_final: 0.7993 (mtp-110) REVERT: C 168 ARG cc_start: 0.7657 (mtt180) cc_final: 0.6720 (ttp-110) REVERT: C 195 GLU cc_start: 0.8725 (mm-30) cc_final: 0.8276 (mm-30) REVERT: C 224 ARG cc_start: 0.8459 (mtt90) cc_final: 0.7911 (mtp-110) REVERT: D 15 ASN cc_start: 0.8710 (m-40) cc_final: 0.8353 (t0) REVERT: D 168 ARG cc_start: 0.7705 (mtt180) cc_final: 0.7058 (ttp-110) REVERT: D 180 ASN cc_start: 0.8057 (m-40) cc_final: 0.7425 (p0) REVERT: D 195 GLU cc_start: 0.8573 (mm-30) cc_final: 0.8203 (mm-30) REVERT: D 224 ARG cc_start: 0.8599 (mtt90) cc_final: 0.7967 (mtp-110) outliers start: 17 outliers final: 12 residues processed: 133 average time/residue: 0.2227 time to fit residues: 39.3546 Evaluate side-chains 133 residues out of total 824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 121 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 148 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 76 optimal weight: 7.9990 chunk 12 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 82 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 84 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 15 optimal weight: 0.5980 chunk 72 optimal weight: 6.9990 chunk 4 optimal weight: 5.9990 chunk 59 optimal weight: 0.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.105744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.074389 restraints weight = 26862.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.076516 restraints weight = 15764.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.077784 restraints weight = 11435.225| |-----------------------------------------------------------------------------| r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.4780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8096 Z= 0.216 Angle : 0.761 14.156 10932 Z= 0.363 Chirality : 0.037 0.172 1300 Planarity : 0.004 0.043 1468 Dihedral : 3.555 16.055 1148 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 16.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Rotamer: Outliers : 2.06 % Allowed : 25.36 % Favored : 72.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.42 (0.25), residues: 1032 helix: 1.92 (0.15), residues: 984 sheet: None (None), residues: 0 loop : -5.18 (0.71), residues: 48 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 4 TYR 0.009 0.002 TYR B 24 ARG 0.012 0.000 ARG D 202 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1687.94 seconds wall clock time: 30 minutes 40.79 seconds (1840.79 seconds total)